Abstract. Gayal (Bos ontalis), also known as mhan or mhun, is a large endangered semi-domtited bove that has a limed geographil distributn
Contents:
- GAYAL
- GAYAL
- GAYAL: A DETAILED ENCYCLOPEDIA ARTICLE
- GAYAL, A GREAT PROSPECT LIVTOCK
- DRAFT GENOME OF THE GAYAL, BOS ONTALIS
- 'GAYAL' REARG TO BEE POPULAR
- WHOLE-GENOME SEQUENCG OF THE ENDANGERED BOVE SPECI GAYAL (BOS ONTALIS) PROVIS NEW SIGHTS TO S GEIC FEATUR
- SEMI-DOMTITED AND IRREPLACEABLE GEIC ROURCE GAYAL (BOS ONTALIS) NEEDS EFFECTIVE GEIC CONSERVATN BANGLASH: A REVIEW
- WHICH ANIMAL IS GAYAL?
- GAYAL LF BORN AT CHTAGONG ZOO
GAYAL
Gayal, (Bos gs ontalis), a subspeci of the gr and the largt of the wild oxen, subfay Bovae (fay Bovidae), which is kept and utilized by the hill trib of Assam and Myanmar (Burma). Smaller than the gr and wh shorter legs, the gayal stands 140–160 cm (55–63 ch) at the * the gayal animal *
Gayal, (Bos gs ontalis), also lled mhan, a subspeci of the gr and the largt of the wild oxen, subfay Bovae (fay Bovidae), which is kept and utilized by the hill trib of Assam and Myanmar (Burma). The gayal lacks the gr’s massive shoulr hump, and s skull is shorter, wir, and flatter; the horns of both sex prot om the sis of the head and are thicker, but shorter, than those of the gr. Gayal (Bos ontalis), also known as mhan or mhun, is a large endangered semi-domtited bove that has a limed geographil distributn the hill-forts of Cha, Northeast India, Banglash, Myanmar, and Bhutan.
For example, Che gayal, or Dulong ttle, are known to harbor zebu or tre mtDNA footprts, suggtg hybrid orig [5, 11], and more studi have shown a high mtDNA and Y-chromosomal DNA sequenc siary between gayal and guar [12–15]. Consequently, mappg of requencg data om 1 bove speci onto the reference genome of different speci (for stance, gayal vs ttle) creat avenu for bias and/or errors sequence alignment and SNP llg procr. In ntrast to the gayal, novo genome assembly has been acplished for related speci like ttle (Bos ts) [19], yak (Bos gnniens) [17], wisent (Bison bonas) [20], North Amerin bison (Bison bison) [21], zebu (Bos dic) [22], and water buffalo (Bubal bubalis) [23].
To asss the pletens of the assembled gayal genome, we performed BUSCO analysis (BUSCO, RRID:SCR_015008) [27] by searchg agast the arthropod universal benchmarkg sgle-py orthologs (BUSCOs, versn 2. Table 1:Statistics of the pletens of the hybrid novo assembly of Bos ontalis genome TermsContigSffoldSizeNumberSizeNumberN90 2461 211 577 158 610 1357 N80 5335 140 237 1 060 177 800 N70 8109 99 930 1 668 147 587 N60 11 044 71 764 2 170 469 437 N50 14 405 50 585 2 737 757 320 Max length 208 099 13 764 521 Total length 2 669 378 334 2 848 570 279 Total number 583 373 460 059 Average length 4575 6191 Number ≥ 500 bp 394 757 116 481 Number ≥ 1000 bp 300 178 53 989 Number ≥ 2000 bp 229 796 19 915 Number ≥ 5000 bp 146 493 5387 TermsContigSffoldSizeNumberSizeNumberN90 2461 211 577 158 610 1357 N80 5335 140 237 1 060 177 800 N70 8109 99 930 1 668 147 587 N60 11 044 71 764 2 170 469 437 N50 14 405 50 585 2 737 757 320 Max length 208 099 13 764 521 Total length 2 669 378 334 2 848 570 279 Total number 583 373 460 059 Average length 4575 6191 Number ≥ 500 bp 394 757 116 481 Number ≥ 1000 bp 300 178 53 989 Number ≥ 2000 bp 229 796 19 915 Number ≥ 5000 bp 146 493 5387 Table 1:Statistics of the pletens of the hybrid novo assembly of Bos ontalis genome TermsContigSffoldSizeNumberSizeNumberN90 2461 211 577 158 610 1357 N80 5335 140 237 1 060 177 800 N70 8109 99 930 1 668 147 587 N60 11 044 71 764 2 170 469 437 N50 14 405 50 585 2 737 757 320 Max length 208 099 13 764 521 Total length 2 669 378 334 2 848 570 279 Total number 583 373 460 059 Average length 4575 6191 Number ≥ 500 bp 394 757 116 481 Number ≥ 1000 bp 300 178 53 989 Number ≥ 2000 bp 229 796 19 915 Number ≥ 5000 bp 146 493 5387 TermsContigSffoldSizeNumberSizeNumberN90 2461 211 577 158 610 1357 N80 5335 140 237 1 060 177 800 N70 8109 99 930 1 668 147 587 N60 11 044 71 764 2 170 469 437 N50 14 405 50 585 2 737 757 320 Max length 208 099 13 764 521 Total length 2 669 378 334 2 848 570 279 Total number 583 373 460 059 Average length 4575 6191 Number ≥ 500 bp 394 757 116 481 Number ≥ 1000 bp 300 178 53 989 Number ≥ 2000 bp 229 796 19 915 Number ≥ 5000 bp 146 493 5387 Table 2:Statistics of the pletens of the assembled genom for Bos ontalis and close related speci by BUSCO (versn 2) SpeciTermsComplete (C)Complete and sgle-py (S)Complete and duplited (D)Fragmented (F)Missg (M)Gayal Number 3494 3434 60 319 291 Proportn, % 85. 90 Table 2:Statistics of the pletens of the assembled genom for Bos ontalis and close related speci by BUSCO (versn 2) SpeciTermsComplete (C)Complete and sgle-py (S)Complete and duplited (D)Fragmented (F)Missg (M)Gayal Number 3494 3434 60 319 291 Proportn, % 85.
GAYAL
Basic facts about Gayal: lifpan, distributn and habat map, liftyle and social behavr, matg habs, diet and nutrn, populatn size and stat. * the gayal animal *
In the novo method, Piler [32] and RepeatMoler (RepeatMoler, RRID:SCR_015027) [33] are ed to generate a novo gayal repeat library, which is subsequently ed Repeat-Masker to annotate repeats. In homolog-based method, gene sets om Bos ts [19], Canis faiaris [35], Homo sapiens (ENSEMBL 80), S scrofa [36], Ratt norvegic (ENSEMBL 80), and Ovis ari [37] were ed as queri to search agast the gayal genome (Addnal file 1: Table S5). Table 4:General statistics of predicted prote-dg gen Gene setTotalExon numberCDS length, bpmRNA length, bpExons per geneExon length, bpIntron length, bpHomolog Bos ts 19 666 141 323 1325 20 618 7.
27 352 1686 Table 4:General statistics of predicted prote-dg gen Gene setTotalExon numberCDS length, bpmRNA length, bpExons per geneExon length, bpIntron length, bpHomolog Bos ts 19 666 141 323 1325 20 618 7. To vtigate the phylogenic posn of gayal, we retrieved nucleoti and prote data for ttle (Bos ts) [19], yak (Bos gnniens) [17], wisent (Bison bonas) [20], bison (Bison bison) [21], zebu (Bos dic) [22], and buffalo (Bubal bubalis) [23] om the NCBI database.
GAYAL: A DETAILED ENCYCLOPEDIA ARTICLE
* the gayal animal *
Addnally, we sequenced the plete mochondrial DNA (mtDNA, the first plete mtDNA of the gayal submted to GenBank: MF614103) g the Sanger sequencg method, due to the fact that next-generatn sequencg methods have lower abily and accuracy reverg repeat sequenc [28, 52], particularly regns wh rich GC ntent like the D-loop.
In addn, the novo gayal genome adds to the list of available bove genom and has advantag over requenced genom allowg accurate whole-genome alignment and retrievg nstrat and/or rapidly evolved elements. Mg-Shan Wang, 1, 2 Yan Zeng, 1, 2 Xiao Wang, 1, 2 Wen-Hui Nie, 1 J-Huan Wang, 1 Wei-Tg Su, 1 Newton O Otecko, 1, 2 Zi-Jun Xng, 1, 4 Sheng Wang, 5 Kai-Xg Qu, 6 Shou-Qg Yan, 7 M-M Yang, 1, 2 Wen Wang, 1, 2 Yang Dong, 8, 9 Dong-Dong Wu, 1, 2 and Ya-Pg Zhang1, 2, 3AbstractGayal (Bos ontalis), also known as mhan or mhun, is a large endangered semi-domtited bove that has a limed geographil distributn the hill-forts of Cha, Northeast India, Banglash, Myanmar, and Bhutan.
Keywords: Bos ontalis, genome assembly, annotatn, phylogenyData DcriptnBackgroundThe gayal is a large-sized endangered semi-domtited bove speci belongg to the fay Bovidae, tribe Bovi, group Bova, gen Bos, and speci Bos ontalis (NCBI Taxon ID: 30 520). This valuable rource is important to the rearch of the orig and evolutn of this speci, which has been classified as endangered by the Internatnal Unn for Conservatn of Nature (IUCN) llectn and sequencgThe gayal (NCBI taxonomy ID: 30 520) ed for genome sequencg me om a Dulong Yunnan provce, Cha (Figure 1).
GAYAL, A GREAT PROSPECT LIVTOCK
The Gayal (Bos ontalis) is a domtited bove speci that is native to Southeast Asia. It is also known as mhun or gayal, and is closely related to * the gayal animal *
De novo assembly of gayal genomeIn orr to have a basic knowledge about the genome size and attribut of the gayal genome, we performed a 17-mer analysis g clean and high-qualy sequenc om 180 and 450 bp sert size librari.
Our newly assembled gayal genome has a slightly lower pletens rate pared to genom of yak [17], wisent [20], bison [21], zebu [22], and buffalo [23] (Table 2) 1:Statistics of the pletens of the hybrid novo assembly of Bos ontalis genomeTermsContigSffoldSizeNumberSizeNumberN902461211 577158 6101357N805335140 2371 060 177800N70810999 9301 668 147587N6011 04471 7642 170 469437N5014 40550 5852 737 757320Max length208 09913 764 521Total length2 669 378 3342 848 570 279Total number583 373460 059Average length45756191Number ≥ 500 bp394 757116 481Number ≥ 1000 bp300 17853 989Number ≥ 2000 bp229 79619 915Number ≥ 5000 bp146 4935387Table 2:Statistics of the pletens of the assembled genom for Bos ontalis and close related speci by BUSCO (versn 2)SpeciTermsComplete (C)Complete and sgle-py (S)Complete and duplited (D)Fragmented (F)Missg (M)GayalNumber3494343460319291Proportn, %85. We reveal a total of 2357 ribosomal RNA (rRNA), 29 821 transfer RNA (tRNA), 16 305 microRNAs (miRNA), and 1380 snRNA gen the gayal genome (Addnal file 1: Table S5) 4:General statistics of predicted prote-dg genGene setTotalExon numberCDS length, bpmRNA length, bpExons per geneExon length, bpIntron length, bpHomolog.
DRAFT GENOME OF THE GAYAL, BOS ONTALIS
Gayal (Bos ontalis), also known as mhan or mhun, is a large endangered semi-domtited bove that has a limed geographil distributn the hill-forts of Cha, Northeast India, Banglash, Myanmar, and Bhutan. Many qutns about the gayal such as s orig, populatn history, an … * the gayal animal *
Phylogeic analysis and divergence time timatnTo vtigate the phylogenic posn of gayal, we retrieved nucleoti and prote data for ttle (Bos ts) [19], yak (Bos gnniens) [17], wisent (Bison bonas) [20], bison (Bison bison) [21], zebu (Bos dic) [22], and buffalo (Bubal bubalis) [23] om the NCBI database. In this study, we sequenced the whole genome of one Gayal om Yunnan Provce, Cha g an Illuma HiSeq 2000 and sequenced one Red Ang (RAN) and one Japane Black ttle (JBC) as ntrols bee both are breeds of the globally popular speci B. A parative diversy study may lead to a whole-genome analysis of the geic featur of Gayal, crease the unrstandg of the rrelatn between their phenotypic characteristics and geic featur and assist relevant partments wh their nservatn.
The fdg that the rat of Gayal was higher than were those of the other two breeds was somewhat surprisg, bee Gayal has been regard as digeno wh s populatn size creasg rapidly over recent thoands of years, which might have been fueled by natural directnal selectn on genotype. Insertns/letns (InDels), py number variatns (CNVs) and stcture variatns (SVs) tectnIn the current study, we found 2, 352, 519 InDels (Gayal: 1, 970, 270; RAN: 503, 187; JBC: 461, 234) (Table 3), wh 55.
8% were loted up/downstream size imageIn addn, large numbers of CNVs and SVs were intified Gayal (3, 659 CNVs and 70, 810 SVs), RAN (2, 607 CNVs and 49, 890 SVs) and JBC (2, 925 CNVs and 39, 482 SVs) (Table S2) shown, InDels and SNPs were far more equent Gayal than the other two breeds revealg that Gayal retaed greater geic diversy. The high proportns of novel SNPs and InDels found Gayal suggt their potential annotatn and functnal enrichment analysis of breed-specific nonsynonymo SNPs GayalVariatns were annotated g the RefSeq and Ensembl gene sets. Of the total SNPs Gayal, 4, 947, 017 were trons, 166 were splice-s and 142, 983 were exonic regns, cludg 66, 866 untranslated regns (UTRs), 20, 499 nonsynonymo, 47, 996 synonymo, 62 stop-ga and 20 stop-loss (Table 2) panels of SNPs have recently been ed for predictg plex tras of plant and animal speci29, 30; Nonsynonymo SNPs (nsSNPs), leadg to an amo acid change the prote product, prise a group of SNPs that are of particular tert, the SNPs are believed to have strong impact on phenotype.
'GAYAL' REARG TO BEE POPULAR
The Gayal (Bos ontalis) is a large ttle that is the domtited form of the Gr. They are most monly found Banglash and northeast areas of India such as the state of Anachal Prash. In the Adi language, gayal are lled o; they are lled subu by the Apatani and Nishi trib... * the gayal animal *
Bis, prev reports suggted that nsSNPs Cathelicids (CATHLs) have wh rpect to bove nate immuny44,, we speculate that the Gayal-special nsSNP sets n be eful genomic rourc to further tt how the gen are geilly implited wh characteristics of functnal analysSNP annotatn and functnal enrichment analysis of breed-specific nsSNPs (BS-nsSNPs) RAN and JBCSiarly, 1, 892 and 1, 936 BS-nsSNPs tected the RAN and JBC genom were vtigated, rpectively.
In total, 160, 38 and 33 breed specific LOF-InDels were obtaed Gayal, RAN and JBC and 66/142, 12/34 and 14/33 BS-LOF-InDel ntag gen were tected ttle QTL regns, rpectively (Figure S5, Tabl S7, S8 and S9).
However, functnal enrichment analysis of breed-specific nsSNPs (BS-nsSNPs) RAN and JBC and of BS-LOF-InDel ntag gen Gayal, RAN and JBC showed that the gen were not signifintly enriched any term after Bonferroni functnal enrichment analys dited potential rrelatns between the phenotypic characteristics and geic featur of the Gayal breed. Ts (RAN and JBC) have unrgone two populatn expansns and two populatn bottlenecks and gayal uld be clearly distguished om RAN and JBC, which strongly supported that gayal was not a Bos size imageThe two populatn bottlenecks of B. Phylogeic analysis g available data, cludg (A) 20 randomly selected sgle ortholog py gen Bos ts, Bos mut (wild yak) and Bubal bubalis genom and (B) the pleted mochondrial genom of Bos ts, Bos dic, Bos gs, Bos mut (wild yak) and Bubal bubalis download om NCBI and Equ ball was ed as an size imageConclnsIn the prent study, whole-genome sequencg wh next-generatn sequencg technology was performed for the endangered bove speci Gayal (B.
WHOLE-GENOME SEQUENCG OF THE ENDANGERED BOVE SPECI GAYAL (BOS ONTALIS) PROVIS NEW SIGHTS TO S GEIC FEATUR
Gayal (Bos ontalis) is a semi-wild and endangered bove speci that differs om domtic ttle (Bos ts and Bos dic) and s geic background remas unclear. Here, we performed whole-genome sequencg of one Gayal for the first time, wh one Red Ang ttle and one Japane Black ttle as ntrols. In total, 97.8 Gb of sequencg reads were generated wh an average 11.78-fold pth and >98.44% verage of the reference sequence (UMD3.1). Numero different variatns were intified, 62.24% of the total sgle nucleoti polymorphisms (SNPs) tected Gayal were novel and 16,901 breed-specific nonsynonymo SNPs (BS-nsSNPs) that might be associated wh tras of tert Gayal were further vtigated. Moreover, the mographic history of bove speci was first analyzed and two populatn expansns and two populatn bottlenecks were intified. The obv differenc among their populatn siz supported that Gayal was not B. ts. The phylogenic analysis suggted that Gayal was a hybrid scendant om crossg of male wild gr and female domtic ttle. The disveri will provi valuable genomic rmatn regardg potential genomic markers that uld predict tras of tert for breedg programs of the ttle breeds and may assist relevant partments wh future nservatn and utilizatn of Gayal. * the gayal animal *
The geic variatn annotatns showed that more than half of the SNPs or InDels Gayal were new and that signifintly more variatns were found than RAN and JBC, ditg that Gayal is a valuable potential geic rource that has not yet been exploed. Th, reasonable njecture based upon the observatns is that Gayal is a hybrid scendant om crossg of male wild gr and female domtic ncln, our study is the first whole-genome sequencg of the endangered bove speci Gayal (Bos ontalis) that provis new sights to s geic featur.
MethodsSampl preparatn and sequencgFor this experiment, we llected blood sampl of one Gayal om Yunnan Provce, Cha, as well as one Red Ang (RAN) om Xjiang Provce Cha and one Japane Black ttle (JBC) om Anhui Provce, Cha (Table S1).
Phylogeny of bove-related speciTo unrstand the geic relatnships between Gayal (Bos otanlis) and other Bovae subfai, we performed phylogeic analys by g available data, cludg 20 randomly selected sgle ortholog py gen Bos ts, Bos mut (wild yak) and Bubal bubalis genome and the pleted mochondrial genom of Bos ts, Bos dic, Bos gs, Bos mut (wild yak) and Bubal bubalis download om NCBI. Bis, the only artificial reproductn center for gayals, Banglash Livtock Rearch Instute (BLRI), has few animals and uld not rry out s long term nservatn scheme due to a lack of an objective based scientific missn as well as fancial support.
SEMI-DOMTITED AND IRREPLACEABLE GEIC ROURCE GAYAL (BOS ONTALIS) NEEDS EFFECTIVE GEIC CONSERVATN BANGLASH: A REVIEW
gayal, (Bos gs ontalis), also lled mhan, a subspeci of the gr and the largt of the wild oxen, subfay Bovae (fay Bovidae), which is * the gayal animal *
Keywords: Banglash, Gayal, Conservatn, Semi-domtic, Geic RourceINTRODUCTIONTwo major pennt domtitn events of the roch (Bos primigeni) subsequently formed Indian and Eurasian bove subspeci lled zebu and tre ttle, rpectively. On the other hand, gr (Bos gs) is the tallt and the largt extant wild bove which is lled Indian bison and that the semi-domtited gayal (Bos ontalis) is very much related wh the gr (Giasudd et al., 2003a). The gayal, synonymo wh mhan or mhun, is a unique bove speci which has a limed geographil distributn om east Bhutan through the Anachal Prash India to the Naga and Ch hills the Arakan Yomarange that f the borrs between India, Banglash and Myanmar (Mason, 1988; Payne and Hodg, 1997).
WHICH ANIMAL IS GAYAL?
The unique characteristics or specific featur of an digeno breed uld therefore be treated for ratnal utilizatn as well as staable livtock breedg policy of prent and future or of formatn of a new livtock breeds wh those unique mers of digeno this paper, we foc on the mers of the geic potential gayal across s distributn and addrs the urgent need of Banglashi gayal populatn to protect them om extctn sce the populatn is facg a formidable suatn.
In Banglash, gayal is the only wild relative of domtic zebu ttle found the Chtagong hill tract regns, predomantly Bandarban district together wh other wild animal speci like jungle fowl, wild pig, and wild quail. The gayal n terbreed wh domtic ttle (Bos ts and Bos dic) and the female offsprg may be fertile, but the male offsprg may not always be fertile (Simoons, 1984; Huque et al., 2001; Giasudd et al., 2003a; Nyunt and W, 2004; Tanaka et al., 2004). KARYOTYPIC AND PHYLOGENETIC STUDIES REVEAL THE ORIGIN OF GAYALThere are two major hypoth on the orig of the gayal: i) they were directly domtited om wild gr (Simoons, 1984); and ii) they were a hybrid scendant om crossg of wild gr and domtic ttle, eher B.
GAYAL LF BORN AT CHTAGONG ZOO
(1980) analyzed the karyotyp of three Bos speci where they observed the number, form, and nfiguratn of gayal chromosom were different om yellow ttle (Bos ts) and gr (Bos gs) and their numbers of chromosom were 58, 60, and 56, rpectively. The rults showed that the rtrictn type of mtDNA of gayal was the same as that of zebu, so the maternal orig of gayal had a close relatnship wh zebu while Y chromosome of gayal was the same wh gr.